Yes, in the exact same way as XCode 3 supports targetting older version with the current SDK: simply set the Deployment Target (yes, I know the example they give is Mac OSX but it works exactly the same on iOS).
Weird question there, because, it supports every iOS since the beginning.
So, u can program for 3.1.3 also in ur Xcode 4
Good luck (it's matter of putting some flags in ur build config). and using non deprecated methods